Elaborate plumage patterning in a Cretaceous bird

Integumentary patterns and colors can differentiate species, sexes, and life changes and can inform on habitat and ecology. However, they are rarely preserved in the fossil record. Here, we report on an extremely well-preserved specimen of the Cretaceous bird Confuciusornis with unprecedented complexity, including small spots on the wings, crest, and throat. Morphological and chemical evidence suggest that these patterns are produced by melanin, but unusual preservation prevents assignment of specific colors. Based on comparisons with extant birds, these patterns were likely used for camouflage, although other functions including sexual signaling cannot be ruled out. Our data show that even more elaborate plumage patterns than the spangles in Anchiornis and stripes in Sinosauropteryx were present at a relatively early stage of avian evolution, showing the significance of coloration and patterning to feather evolution

The fossil record of birds from the James Ross Basin, West Antarctica

The fossil record of birds from Antarctica is concentrated in the James Ross Basin, located in north-east of the Antarctic Peninsula. Birds are here represented by an extensive Paleogene record of penguins (Sphenisciformes) and Cretaceous–Paleogene record of Anseriformes, followed by other groups with a minor representation (Procellariiformes, Falconiformes, and Pelagornithidae), and others previously assigned controversially to “Ratites”, Threskiornithidae, Charadriiformes, Gruiformes, Phoenicopteriformes, and Gaviiformes. We provide a complete update of these records, commenting on the importance of some of these remains for the evolution of the major clades.Fil: Acosta Hospitaleche, Carolina Ileana Alicia. Universidad Nacional de La Plata. Facultad de Ciencias Naturales y Museo. División Paleontología Vertebrados; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata; ArgentinaFil: Jadwiszczak, Piotr. University Of Bialystok; PoloniaFil: Clarke, Julia A.. University of Texas at Austin; Estados UnidosFil: Cenizo, Marcos. Museo de Historia Natural de La Pampa, División Paleontología; Argentina. Fundación de Historia Natural Félix de Azara; Argentin

Accuracy of non-invasive prenatal testing using cell-free DNA for detection of Down, Edwards and Patau syndromes : a systematic review and meta-analysis

Objective: To measure test accuracy of non-invasive prenatal testing (NIPT) for Down, Edwards and Patau syndromes using cell-free fetal DNA and identify factors affecting accuracy. Design: Systematic review and meta-analysis of published studies. Data sources: PubMed, Ovid Medline, Ovid Embase and the Cochrane Library published from 1997 to 9 February 2015, followed by weekly autoalerts until 1 April 2015. Eligibility: Criteria for selecting studies English language journal articles describing case–control studies with ≥15 trisomy cases or cohort studies with ≥50 pregnant women who had been given NIPT and a reference standard. Results: 41, 37 and 30 studies of 2012 publications retrieved were included in the review for Down, Edwards and Patau syndromes. Quality appraisal identified high risk of bias in included studies, funnel plots showed evidence of publication bias. Pooled sensitivity was 99.3% (95% CI 98.9% to 99.6%) for Down, 97.4% (95.8% to 98.4%) for Edwards, and 97.4% (86.1% to 99.6%) for Patau syndrome. The pooled specificity was 99.9% (99.9% to 100%) for all three trisomies. In 100 000 pregnancies in the general obstetric population we would expect 417, 89 and 40 cases of Downs, Edwards and Patau syndromes to be detected by NIPT, with 94, 154 and 42 false positive results. Sensitivity was lower in twin than singleton pregnancies, reduced by 9% for Down, 28% for Edwards and 22% for Patau syndrome. Pooled sensitivity was also lower in the first trimester of pregnancy, in studies in the general obstetric population, and in cohort studies with consecutive enrolment. Conclusions: NIPT using cell-free fetal DNA has very high sensitivity and specificity for Down syndrome, with slightly lower sensitivity for Edwards and Patau syndrome. However, it is not 100% accurate and should not be used as a final diagnosis for positive cases

Fossil record of penguins.

77 p. : ill., map ; 26 cm. "Issued June 3, 2010." Includes bibliographical references (p. 47-53).We present the first detailed description of Perudyptes devriesi, a basal penguin from the middle Eocene (~42 Ma) Paracas Formation of Peru, and a new analysis of all published extinct penguin species as well as controversial fragmentary specimens. The Perudyptes devriesi holotype includes key regions of the skull and significant postcranial material, thus helping to fill a major phylogenetic and stratigraphic (~20 million year) gap between the earliest fossil penguins (Waimanu manneringi and Waimanu tuatahi, ~58-61.6 Ma) and the next oldest partial skeletons. Perudyptes devriesi is diagnosable by five autapomorphies: (1) an anteroventrally directed postorbital process, (2) marked anterior expansion of the parasphenoid rostrum, (3) posterior trochlear ridge of the humerus projecting distal to the middle trochlear ridge and conformed as a large, broadly curved surface, (4) convex articular surface for the antitrochanter of the femur, and (5) extremely weak anterior projection of the lateral condyle of the tibiotarsus. The skull of Perudyptes is characterized by deep temporal fossae and an elongate, narrow beak that differs from other reported stem penguins in its short mandibular symphysis. The wing skeleton of Perudyptes preserves a combination of plesiomorphic features also observed in the basal penguin Waimanu and derived features shared with more crownward penguins. Features of the wing optimized as primitive for Sphenisciformes include retention of a discrete dorsal supracondylar tubercle on the humerus and presence of a modestly projected pisiform process on the carpometacarpus. Derived features present in Perudyptes and all more crownward penguins, but absent in Waimanu, include a more flattened humerus, development of a trochlea for the tendon of m. scapulotriceps at the distal end of the humerus, and bowing of the anterior face of the carpometacarpus. A combined molecular and morphological dataset for Spheniciformes was expanded by adding 25 osteological and soft tissue characters as well as 11 taxa. In agreement with previous results, Perudyptes devriesi is identified as one of the most basal members of Sphenisciformes. This analysis also confirms the placement of the middle/late Miocene (~11-13 Ma) fossil Spheniscus muizoni as a member of the Spheniscus clade and places the late Miocene (~10 Ma) Madrynornis mirandus as sister taxon to extant Eudyptes. These two species, known from relatively complete partial skeletons, are the oldest crown clade penguin fossils and represent well-corroborated temporal calibration points for the Spheniscus-Eudyptula divergence and Megadyptes-Eudyptes divergence, respectively. Our results reaffirm that the Miocene penguin taxon Palaeospheniscus, recently proposed to represent a member of the crown radiation, belongs outside of the crown clade Spheniscidae. The phylogenetic positions of small Eocene Antarctic penguin taxa (Delphinornis, Marambiornis, and Mesetaornis) recently proposed as possible direct ancestors to crown Spheniscidae were further evaluated using alternate coding strategies for incorporating scorings from isolated elements that preserve critical morphologies and are thought to represent these taxa, although they cannot yet be reliably assigned to individual species. Under all scoring regimes, Delphinornis, Marambiornis, and Mesetaornis were recovered as distantly related to Spheniscidae. Using synapomorphies identified in the primary analysis, we evaluated the phylogenetic position of fragmentary specimens, including the holotypes of valid but poorly known species, specimens currently unassignable to the species level, and morphologically distinct specimens that have not yet been named. All pre-Miocene specimens can be excluded from Spheniscidae based on presence of plesiomorphies lost in all crown penguins, consistent with a recent radiation for the penguin crown clade. This study provides additional support for a scenario of penguin evolution characterized by an origin of flightlessness near the K-T boundary, dispersal throughout the Southern Hemisphere during the early Paleogene, and a late Cenozoic origin for the crown clade Spheniscidae. Stratigraphic distribution and phylogenetic relationships of fossil penguins are consistent with distinct radiations during the Eocene, Oligocene, and Miocene. While the Eocene and Oligocene penguin faunas are similar in many respects, the Miocene fauna is characterized by smaller average size and novel cranial morphologies, suggesting that an ecological shift in diet occurred close to the origin of crown Spheniscidae

Feather development genes and associated regulatory innovation predate the origin of Dinosauria

The evolution of avian feathers have recently been illuminated by fossils and the identification of genes involved in feather patterning and morphogenesis. However, molecular studies have focused mainly on protein-coding genes. Using comparative genomics and more than 600,000 conserved regulatory elements, we show that patterns of genome evolution in the vicinity of feather genes are consistent with a major role for regulatory innovation in the evolution of feathers. Rates of innovation at feather regulatory elements exhibit an extended period of innovation with peaks in the ancestors of amniotes and archosaurs. We estimate that 86% of such regulatory elements were present prior to the origin of Dinosauria. On the branch leading to modern birds, we detect a strong signal of regulatory innovation near IGFBP2 and IGFBP5, which have roles in body size reduction, and may represent a genomic signature for the miniaturization of dinosaurian body size preceding the origin of flight.Organismic and Evolutionary Biolog

Ichthyornis and Apatornis

179 p. : ill. ; 26 cm.Includes bibliographical references (p. 157-167).Charles Darwin commented that Ichthyornis, as one of the "toothed birds" from the late Cretaceous of Kansas, offered some of "the best support to the theory of evolution" (in litt., C. Darwin to O.C. Marsh, August 31, 1880). Ichthyornis figures no less prominently today. It is one of the closest outgroups to crown clade Aves, and remains one of the only Mesozoic avialans known from more than a handful of specimens. As such, Ichthyornis is an essential taxon for analyses of deep divergences within Aves because of its influence in determining the morphologies ancestral to the crown clade. Ichthyornis, however, has languished in need of new anatomical description and taxonomic revision. Many of the best Ichthyornis specimens were largely inaccessible, plastered into Yale Peabody Museum (YPM) exhibit mounts for nearly a century. The focus of this study was the entire YPM Ichthyornis collection, the largest at any institution. The elements removed from the mounts were identified to the specimens with which they were originally associated. Detailed morphological study of the 81 YPM specimens yielded the following results: (1) there is evidence for only one species of Ichthyornis, rather than the eight previously proposed; (2) 78 specimens are part of this species, Ichthyornis dispar; (3) two previously identified species are not part of Ichthyornis; and (4) one new species is identified. This analysis also provided a case study in the application of phylogenetic nomenclature at the species level. The morphology of Ichthyornis dispar is described in detail from the holotype and referred specimens. Phylogenetic analyses of 202 morphological characters, scored for 24 terminal taxa, evaluated the relationships among Mesozoic ornithurines including Ichthyornis dispar and the newly identified taxa. Analysis of 23 core taxa produced two most parsimonious trees (L: 384, CI: 0.66). Marsh's "Ichthyornithiformes" is not monophyletic: Two previously named species of Ichthyornis as well as Apatornis celer are placed as more closely related to or as part of Aves. The results of the phylogenetic analyses have implications for previous hypotheses of the timing and pattern of the origin of Aves

Fossil penguin

18 p. : ill., maps ; 26 cm.Includes bibliographical references (p. 15-17).We report the discovery of the first vertebrate from the Paleogene of Tierra del Fuego (Isla Grande), Argentina, in southernmost South America. The specimen consists of parts of an associated pelvic girdle and limb that are identified as belonging to the penguin stem clade (Aves: Pansphenisciformes). The specimen, from an exposure of the Leticia Formation (late middle Eocene), is the earliest known penguin (pansphenisciform) from South America. It is more than 20 million years older than the earliest previously recorded South American penguins (from the late Oligocene-early Miocene) and, thus, almost doubles their known record on the continent. A detailed description of the new specimen and a discussion of its implications for the understanding of penguin morphological evolution are provided. The new specimen and other fossil penguins do not currently point to the origin of extant, or crown clade, penguin lineages (Spheniscidae), by the Eocene, only to the divergence of the penguin stem lineage from its sister taxon by this time. The new fossil has several morphologies that differ from all extant penguins but are shared with other fossil penguin taxa, suggesting they may be outside Spheniscidae. However, in a discussion of the current status of penguin systematics, we suggest the urgent need for comprehensive phylogenetic analysis of fossil and extant penguins to clarify the timing and pattern of penguin diversification. The specimen was recovered from a newly identified fossil vertebrate locality, an exposure of the Eocene Leticia Formation at Punta Torcida on the Atlantic shore of southeastern Tierra del Fuego, Argentina. The new locality is introduced, and a brief geologic description is made, highlighting the potential of the shallow marine sediments of the Leticia Formation for contributing to our knowledge of the Paleogene vertebrate fossil record of Tierra del Fuego, and of southern South America, generally

Systematics and phylogeny of the Zygodactylidae (Aves, Neognathae) with description of a new species from the early Eocene of Wyoming, USA

Zygodactylidae are an extinct lineage of perching birds characterized by distinct morphologies of the foot and wing elements. Although the clade has a complex taxonomic history, current hypotheses place Zygodactylidae as the sister taxon to Passeriformes (i.e., songbirds). Given the rather sparse fossil record of early passeriforms, the description of zygodactylid taxa is important for inferring potentially ancestral states in the largest radiation of living birds (i.e., the ∼6,000 species of extant passeriforms). Despite the exceptional preservation of many specimens and considerable species diversity in Zygodactylidae, the relationships among species have not been previously evaluated in a phylogenetic context. Herein, we review the fossil record of Zygodactylidae from North America and describe five new well-preserved fossils from the early Eocene Green River Formation of Wyoming. Two specimens are identified as representing a new species and the first records of the taxon Zygodactylus outside Europe. Anatomical comparisons with previously named taxa and the results of phylogenetic analysis including newly described specimens and previously named zygodactylid taxa provide the first hypothesis of the species-level relationships among zygodactylids. The monophyly of Zygodactylidae is supported in these new analyses. However, the monophyly of Primozygodactylus and the taxonomic distinction between Zygodactylus and Eozygodactylus remain unresolved and would likely benefit from the description of additional specimens

Eocene avian from Mongolia

17 p. : ill., map ; 26 cm.A well-preserved nearly complete avian tarsometatarsus was collected by the 2002 expedition of the Mongolian Academy of Sciences from Upper Eocene deposits exposed at the locality of Alag Tsav in the eastern Gobi Desert (Dornogov Aimag) of Mongolia. The new specimen is identified as part of a proposed Eogruidae clade, although it is unclear whether it is appropriately the holotype of a new species within this clade or referable to a previously named species. The clade Eogruidae has, as its current contents, species named as part of the traditional families Eogruidae + Ergilornithidae, which include several taxa of completely didactylous and apparently flightless birds. Referral of the new fossil to the clade Eogruidae is on the basis of derived reduction/loss of the metatarsal II trochlea. A series of phylogenetic analyses was used to investigate the systematic position of Eogruidae (including the new fossil, IGM 100/1447), which have been proposed to be a dominant part of Eocene to Miocene Asian faunas. First, the Mayr and Clarke (2003) dataset for crown clade Aves was used to investigate placement of Eogruidae within Aves, using a more completely known eogruid, Eogrus aeola, as an exemplar taxon. Eogrus aeola was identical to the new tarsometatarsus for all scored characters. A strict consensus cladogram of three most parsimonious trees from 1000 replicate heuristic searches placed Eogrus aeola in an unresolved polytomy with Psophiidae and Gruidae (trumpeters and cranes). Given the results of this analysis, Eogruidae (including IGM 100/1447) was analyzed in the suborder Grues dataset of Livezey (1998). Eogruidae was placed as the sister taxon to an Aramidae + Gruidae clade in the strict consensus cladogram of the eight most parsimonious trees resulting from a branch and bound search. Because monophyly of the traditional order Gruiformes has been repeatedly questioned, and the outgroups used in the original Grues dataset were identified through analyses assuming monophyly, the impact of removing these assumptions was investigated. Placement was robust to both changing outgroup assumptions and to swapping in the more incompletely known IGM 100/1447 as an exemplar for Eogruidae

A bony-crested Jurassic dinosaur with evidence of iridescent plumage highlights complexity in early paravian evolution

The Jurassic Yanliao theropods have offered rare glimpses of the early paravian evolution and particularly of bird origins, but, with the exception of the bizarre scansoriopterygids, they have shown similar skeletal and integumentary morphologies. Here we report a distinctive new Yanliao theropod species bearing prominent lacrimal crests, bony ornaments previously known from more basal theropods. It shows longer arm and leg feathers than Anchiornis and tail feathers with asymmetrical vanes forming a tail surface area even larger than that in Archaeopteryx. Nanostructures, interpreted as melanosomes, are morphologically similar to organized, platelet-shaped organelles that produce bright iridescent colours in extant birds. The new species indicates the presence of bony ornaments, feather colour and flight- related features consistent with proposed rapid character evolution and significant diversity in signalling and locomotor strategies near bird origins